Tuesday 10 September 2013 12.40 EDT
First published on Tuesday 10 September 2013 12.40 EDT

This actually happened yesterday:

A professor in the computer science department at Johns Hopkins, a leading American university, had written a post on his blog, hosted on the university's servers, focused on his area of expertise, which is cryptography. The post was highly critical of the government, specifically the National Security Agency, whose reckless behavior in attacking online security astonished him.

The post was widely circulated online because it is about the sense of betrayal within a community of technical people who had often collaborated with the government. (I linked to it myself.)

On Monday, he gets a note from the acting dean of the engineering school asking him to take the post down and stop using the NSA logo as clip art in his posts. The email also informs him that if he resists he will need a lawyer. The professor runs two versions of the same site: one hosted on the university's servers, one on Google's blogger.com service. He tells the dean that he will take down the site mirrored on the university's system but not the one on blogger.com. He also removes the NSA logo from the post. Then, he takes to Twitter.

I received a request from my Dean this morning asking me to remove all copies of my NSA blog post from University servers.

The professor says he was told that someone at the Applied Physics Laboratory, a research institute with longstanding ties to the Department of Defense and the National Security Agency, determined that his blog post was hosting or linking to classified material, and sounded the alarm, which led to the takedown request from the dean. He says he thought Johns Hopkins University, his employer, had come down "on the wrong side of common sense and academic freedom", particularly since the only classified material he had linked to was from news reports in the Guardian, the New York Times and ProPublica.org – information available to the public.

Word gets around, and by late afternoon, the press starts asking questions. Now, Johns Hopkins is worried about how it looks in the media. The university bureaucracy scrambles the jets and comes up with a statement:

The university received information this morning that Matthew Green's blog contained a link or links to classified material and also used the NSA logo. For that reason, we asked professor Green to remove the Johns Hopkins-hosted mirror site for his blog Upon further review, we note that the NSA logo has been removed and that he appears to link to material that has been published in the news media. Interim Dean Andrew Douglas has informed professor Green that the mirror site may be restored.

So the university backs down, leaving many unanswered questions. Possibly, they will be addressed today. (Update: Johns Hopkins dean apologizes.) Here are some on my list:

Who was it in the Applied Physics Laboratory, with its close ties to the NSA, that raised the alarm about what a (very effective) critic of the NSA was writing ... and why?

Did that person hear first from the government and then contact the Johns Hopkins officials?

Why would an academic dean cave under pressure and send the takedown request without careful review, which would have easily discovered, for example, that the classified documents to which the blog post linked were widely available in the public domain?

Why is Johns Hopkins simultaneously saying that the event was internal to the university (that the request didn't come from the government) and that it doesn't know how the whole thing began? The dean of the engineering school doesn't know who contacted him about a professor's blog post? Really? The press office doesn't know how to get in touch with the dean? Seems unlikely. Johns Hopkins spokesman Dennis O'Shea told me this morning that university officials "were still trying to trace" the events back to their source. Clearly, there's a lot more to the story.

Matthew Green said the original request to take down his post could have referred to his Blogger.com site and the site hosted on Johns Hopkins servers. Since a request to unpublish your thoughts is one of the most extreme and threatening that any university can make of a faculty member, what kind of deliberation went into it? That Johns Hopkins backtracked so quickly after the press started asking questions suggests that the reasoning was pretty thin. But the request was momentous. These things don't fit together. What gives?

Dennis O'Shea told me the original concern was that Matthew Green's post might be "illegally linking to classified information". I asked him what law he was referring to. "I'm not saying that there was a great deal of legal analysis done," he replied. Obviously. But again: given the severity of the remedy – unpublishing an expert's post critical of the NSA – careful legal analysis was called for. Why was it missing?

In commenting critically on a subject he is expert in, and taking an independent stance that asks hard questions and puts the responsibility where it belongs, Matthew Green is doing exactly what a university faculty member is supposed to be doing. By putting his thoughts in a blog post that anyone can read and link to, he is contributing to a vital public debate, which is exactly what universities need to be doing more often. Instead of trying to get Matthew Green's blog off their servers, the deans should be trying to get more faculty into blogging and into the public arena. Who at Johns Hopkins is speaking up for these priorities? And why isn't the Johns Hopkins faculty roaring about this issue? (I teach at New York University, and I'm furious.)

Notice: Matthew Green didn't get any takedown request from Google. Only from Johns Hopkins. Think about what that means for the school. He's "their" professor, yet his work is safer on the servers of a private company than his own university. The institution failed in the clutch. That it rectified it later in the day is welcome news, but I won't be cheering until we have answers that befit a great institution like Johns Hopkins, where graduate education was founded on these shores.

And another thing: America's system of research universities is the best in the world. No one argues with that. It's one of biggest advantages this nation has. If it becomes captive to government and handmaiden to the surveillance state, that would be an economic and cultural crime of monstrous proportions. What happened to Matthew Green's blog post yesterday is no small matter.